[gmx-users] hydrogen hydrogen interaction

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 15 03:24:32 CET 2012

bo.shuang wrote:
> Hi, all,
> Does hydrogen hydrogen non-bond interactions be calculated in the 
> simulation? It looks to me this kind of non-bond interaction is ignored. 
> If not, is there a way to let it count h-h interaction? Thank you!

It is common for force fields to assign zero values to LJ terms for H atoms. 
The LJ interactions are largely governed by the heavy atom(s) to which the H 
atoms are connected.  All explicit H atoms in any force field should bear some 
partial charge, and thus H atoms directly participate in Coulombic interactions.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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